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Port details
ddocent Bash pipeline for RAD sequencing
2.7.8_1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 2.7.8Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-04-20 01:34:22
Last Update: 2019-07-26 21:46:57
SVN Revision: 507372
Also Listed In: java perl5 python
License: MIT
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (19 items)
  1. /usr/local/share/licenses/dDocent-2.7.8_1/catalog.mk
  2. /usr/local/share/licenses/dDocent-2.7.8_1/LICENSE
  3. /usr/local/share/licenses/dDocent-2.7.8_1/MIT
  4. bin/ErrorCount.sh
  5. bin/RefMapOpt.sh
  6. bin/ReferenceOpt.sh
  7. bin/Rename_SequenceFiles.sh
  8. bin/Rename_for_dDocent.sh
  9. bin/Rename_for_dDocent_with-INDEX.sh
  10. bin/dDocent
  11. bin/dDocent_filters
  12. bin/dDocent_ngs.sh
  13. bin/ddocent-assembly-test
  14. bin/ddocent-assembly-test-cleanup
  15. bin/filter_hwe_by_pop.pl
  16. bin/filter_missing_ind.sh
  17. bin/pop_missing_filter.sh
  18. bin/remake_reference.sh
  19. bin/remove.bad.hap.loci.sh
Collapse this list.
Dependency lines:
  • dDocent>0:biology/ddocent
To install the port: cd /usr/ports/biology/ddocent/ && make install clean
To add the package: pkg install dDocent
PKGNAME: dDocent
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. python3.6 : lang/python36
  2. perl5>=5.28.r1<5.29 : lang/perl5.28
Runtime dependencies:
  1. unzip>=0 : archivers/unzip
  2. mawk>=0 : lang/mawk
  3. gawk>=0 : lang/gawk
  4. coreutils>=0 : sysutils/coreutils
  5. gnuplot>=0 : math/gnuplot
  6. parallel>=0 : sysutils/parallel
  7. bash : shells/bash
  8. bwa>=0.7.13 : biology/bwa
  9. cd-hit>=0 : biology/cd-hit
  10. samtools>=1.3 : biology/samtools
  11. vcftools>=0.1.15 : biology/vcftools
  12. trimmomatic>=0 : biology/trimmomatic
  13. bamtools>=0 : biology/bamtools
  14. stacks>=0 : biology/stacks
  15. rainbow>=0 : biology/rainbow
  16. trimadap>=0 : biology/trimadap
  17. seqtk>=0 : biology/seqtk
  18. bedtools>=2.26.0 : biology/bedtools
  19. pear-merger>=0 : biology/pear-merger
  20. vcflib>=0 : biology/vcflib
  21. freebayes : biology/freebayes
  22. fastp : biology/fastp
  23. java : java/openjdk8
  24. python3.6 : lang/python36
  25. perl5>=5.28.r1<5.29 : lang/perl5.28
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/jpuritz/dDocent/tar.gz/v2.7.8?dummy=/

Number of commits found: 4

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 Jul 2019 20:46:57
Original commit files touched by this commit  2.7.8_1
Revision:507372
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
04 May 2019 15:09:10
Original commit files touched by this commit  2.7.8
Revision:500812
jwb search for other commits by this committer
biology/ddocent: Upgrade to 2.7.8

Reported by:    portscout
12 Dec 2018 01:35:36
Original commit files touched by this commit  2.2.25_1
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
20 Apr 2018 01:34:05
Original commit files touched by this commit  2.2.25
Revision:467808
jwb search for other commits by this committer
biology/ddocent: Bash pipeline for RAD sequencing

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15139

Number of commits found: 4

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